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- PDB-26va: Biotin-bound SMVT in the occluded state -

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Basic information

Entry
Database: PDB / ID: 26va
TitleBiotin-bound SMVT in the occluded state
ComponentsSodium-dependent multivitamin transporter
KeywordsTRANSPORT PROTEIN / Sodium-dependent multivitamin transporter / SMVT / SLC5A6 / Biotin
Function / homology
Function and homology information


sodium-dependent multivitamin transmembrane transporter activity / pantothenate transmembrane transporter activity / pantothenate:sodium symporter activity / pantothenate transmembrane transport / biotin import across plasma membrane / Transport of vitamins, nucleosides, and related molecules / vitamin transmembrane transporter activity / iodide transmembrane transport / biotin metabolic process / biotin transmembrane transporter activity ...sodium-dependent multivitamin transmembrane transporter activity / pantothenate transmembrane transporter activity / pantothenate:sodium symporter activity / pantothenate transmembrane transport / biotin import across plasma membrane / Transport of vitamins, nucleosides, and related molecules / vitamin transmembrane transporter activity / iodide transmembrane transport / biotin metabolic process / biotin transmembrane transporter activity / biotin transport / iodide transmembrane transporter activity / Vitamin B5 (pantothenate) metabolism / Biotin transport and metabolism / sodium ion transport / transport across blood-brain barrier / basal plasma membrane / brush border membrane / basolateral plasma membrane / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
: / Sodium:solute symporter family signature 1. / Sodium/solute symporter, conserved site / Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile.
Similarity search - Domain/homology
BIOTIN / Sodium-dependent multivitamin transporter
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang, Z. / Zhen, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471252 China
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for multivitamin recognition and transport by human SMVT.
Authors: Qiuxin Zhen / Mingshuai Wang / Zhe Zhang /
Abstract: The human sodium-dependent multivitamin transporter (SMVT, SLC5A6) mediates cellular uptake of essential metabolic cofactors, including biotin, pantothenate, and lipoate. Its dysfunction is ...The human sodium-dependent multivitamin transporter (SMVT, SLC5A6) mediates cellular uptake of essential metabolic cofactors, including biotin, pantothenate, and lipoate. Its dysfunction is associated with neurological disorders, metabolic abnormalities, and cancer. However, the molecular mechanism underlying its multi-substrate transport has remained elusive. Here, we present cryo-electron microscopy structures of human SMVT in three conformational states: occluded, outward-open, and inward-open. These structural snapshots capture the complete transport cycle and reveal a conserved substrate-binding pocket near a kinked transmembrane helix (TM1). Within this pocket, substrate carboxyl groups are electrostatically anchored, while distinct chemical moieties interact with specific polar and hydrophobic residues. Functional assays identify key binding residues and elucidate the pathogenic effects of disease-associated mutations. Further structural analysis delineates the principles of substrate discrimination within the SLC5 transporter family. Together, our work provides a structural framework for SMVT's polyspecificity and lays a foundation for understanding related diseases and developing targeted therapeutic strategies.
History
DepositionMay 16, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 8, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sodium-dependent multivitamin transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2452
Polymers68,0011
Non-polymers2441
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sodium-dependent multivitamin transporter / Na(+)-dependent multivitamin transporter / hSMVT / Solute carrier family 5 member 6


Mass: 68000.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC5A6, SMVT / Production host: Homo sapiens (human) / References: UniProt: Q9Y289
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SMVT in complex with biotin in an occluded conformation
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.07 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5207model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 370720 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0063965
ELECTRON MICROSCOPYf_angle_d0.9225401
ELECTRON MICROSCOPYf_dihedral_angle_d10.1571366
ELECTRON MICROSCOPYf_chiral_restr0.053630
ELECTRON MICROSCOPYf_plane_restr0.008659

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